Had the same problem myself and tried god knows how many permutations. Even took it to my alloy repairer and he couldn't get the damn thing back in and he has a TT!! Then got sick, went to Audi as a discerning punter, opened up the boot and looked in the kit in an A4 cab. The handle tucks in behind with a bit of cajoling, under the main body of the jack so that the main stem of the handle lies flush with the edge of the jack body.
When you go to put it back in the box it is the first part of the jack that goes in and it sits between the jack body and the side wall of the box that is against the wall of the boot well (and the handle stem is therefore visible). A bit of jiggling in and you can close the box again.
But what a faff on, quicker to call out the AA if you get a flat or simply want to chang your tyres around!!